Locus 6605

Sequence ID	3R_DroMel_CAF1
Location	17,378,362 – 17,378,464
Length	102
Max. P	0.942170

overview

Window 2

Location	17,378,362 – 17,378,464
Length	102
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	85.10
Mean single sequence MFE	-21.09
Consensus MFE	-16.29
Energy contribution	-16.10
Covariance contribution	-0.19
Combinations/Pair	1.08
Mean z-score	-2.28
Structure conservation index	0.77
SVM decision value	1.32
SVM RNA-class probability	0.942170
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17378362 102 + 27905053
UUCAGUGCUCUC----CACCACUCCACUGCACAUCCAAGCCCACCUACACGCACACAUCCACAUCCACAUCCCAACCCCCAUUCAUGGGGUCGUUGGCGCGGCCAU
....((((....----............))))......((((........(....)...............((((((((((....)))))..))))).).)))... ( -19.79)
>DroSec_CAF1 27375 94 + 1
UUCAGUGCUCUC------------CACUGCACAUCCAAGCCCACCUACACCCACUCAUCCACAUCGACAUCCCAACCCCCUUUCAUGGGGUCGUUGGCGCGGCCAU
....((((....------------....))))......((((...............((......))....(((((((((......))))..))))).).)))... ( -21.70)
>DroSim_CAF1 36099 102 + 1
UUCAGUGCUCUC----CACCACUCCACUGCACAUCCAAGCCCACCUACACCCACACAUCCACAUCGACAUCCCAACCCCCUUUCAUGGGGUCGUUGGCGCGGCCAU
....((((....----............))))......((((...............((......))....(((((((((......))))..))))).).)))... ( -20.29)
>DroYak_CAF1 43447 99 + 1
UUCAGUGC----CCACCAGCACUCCACUGCACAUCCAGGCU---CUACACCUCCACCUACACAUCCACAUCUCAACCCCCUUUCAUGGGGUCGUUGGCGCGGCCAU
....(.((----((.(((((......(((......)))...---................................((((......))))..))))).).)))).. ( -22.60)
>consensus
UUCAGUGCUCUC____CACCACUCCACUGCACAUCCAAGCCCACCUACACCCACACAUCCACAUCCACAUCCCAACCCCCUUUCAUGGGGUCGUUGGCGCGGCCAU
....((((....................)))).......................................(((((((((......))))..)))))......... (-16.29 = -16.10 +  -0.19)

alignment

secondary structure

dotplot

Window 3

Location	17,378,362 – 17,378,464
Length	102
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	85.10
Mean single sequence MFE	-33.95
Consensus MFE	-24.87
Energy contribution	-25.93
Covariance contribution	1.06
Combinations/Pair	1.08
Mean z-score	-2.12
Structure conservation index	0.73
SVM decision value	0.95
SVM RNA-class probability	0.888442
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17378362 102 - 27905053
AUGGCCGCGCCAACGACCCCAUGAAUGGGGGUUGGGAUGUGGAUGUGGAUGUGUGCGUGUAGGUGGGCUUGGAUGUGCAGUGGAGUGGUG----GAGAGCACUGAA
....((((((((.(((((((.......))))))).....))).)))))...((..(((.((((....)))).)))..))....((((.(.----...).))))... ( -35.90)
>DroSec_CAF1 27375 94 - 1
AUGGCCGCGCCAACGACCCCAUGAAAGGGGGUUGGGAUGUCGAUGUGGAUGAGUGGGUGUAGGUGGGCUUGGAUGUGCAGUG------------GAGAGCACUGAA
..((((.((((..(((((((.......)))))))..((..(.((........)).)..)).))))))))........(((((------------.....))))).. ( -32.10)
>DroSim_CAF1 36099 102 - 1
AUGGCCGCGCCAACGACCCCAUGAAAGGGGGUUGGGAUGUCGAUGUGGAUGUGUGGGUGUAGGUGGGCUUGGAUGUGCAGUGGAGUGGUG----GAGAGCACUGAA
.(.(((((.(((.(((((((.......)))))))..(((((......)))))(((.((.((((....)))).)).)))..))).))))).----)........... ( -31.90)
>DroYak_CAF1 43447 99 - 1
AUGGCCGCGCCAACGACCCCAUGAAAGGGGGUUGAGAUGUGGAUGUGUAGGUGGAGGUGUAG---AGCCUGGAUGUGCAGUGGAGUGCUGGUGG----GCACUGAA
....((((.(((.(((((((.......))))))).....)))...((((.((..((((....---.))))..)).))))))))((((((....)----)))))... ( -35.90)
>consensus
AUGGCCGCGCCAACGACCCCAUGAAAGGGGGUUGGGAUGUCGAUGUGGAUGUGUGGGUGUAGGUGGGCUUGGAUGUGCAGUGGAGUGGUG____GAGAGCACUGAA
..((((.((((..(((((((.......)))))))..(..((.((........)).))..).))))))))........(((((.................))))).. (-24.87 = -25.93 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:40 2006